Chapter 3 – Carbon & The
Molecular Diversity of Life

• Although cells are 70-95% water, the rest consists mostly of carbon-based compounds.
• Proteins, DNA, carbohydrates, and other molecules that distinguish living matter from inorganic material are all composed of carbon atoms bonded to each other and to atoms of other elements.
– These other elements commonly include hydrogen (H), oxygen (O), nitrogen (N), sulfur
(S), and phosphorus (P).

Carbon & Biomass
“Carbon chemistry rules Life …”
“All forms of life on planet Earth and all molecules they produce are based on the chemical element carbon ….”
6
12.01
C
Simplified Bohr Atomic Model of Carbon
-
-
-
-
+
Electron (6)
Proton (6)
Neutron (6,7 or 8)
-

• The study of carbon compounds, organic chemistry , focuses on any compound with carbon (organic compounds).
– While the name, organic compounds, implies that these compounds can only come from biological processes, they can be synthesized by non-living reactions.
– Organic compounds can range from the simple (CO
2 or CH
4
) to complex molecules, like proteins, that may weigh over 100,000 daltons.

• The science of organic chemistry began in attempts to purify and improve the yield of products from other organisms.
– Later chemists learned to synthesize simple compounds in the laboratory, but they had no success with more complex compounds.
– The Swedish chemist Jons J. Berzelius was the first to make a distinction between organic compounds that seemed to arise only in living organisms and inorganic compounds from the nonliving world.
• This lead early organic chemists to propose vitalism , the belief in a life outside the limits of physical and chemical laws.

• Support for vitalism began to wane as organic chemists learned to synthesize more complex organic compounds in the laboratory.
– In the early 1800’s the German chemist
Friedrich Wöhler was able to synthesize urea from totally inorganic starting materials.
• In 1953, Stanley Miller at the
University of Chicago was able to simulate chemical conditions on the primitive Earth to demonstrate the spontaneous synthesis of organic compounds.

• Carbon atoms are the most versatile building blocks of molecules.
• With a total of 6 electrons, a carbon atom has 2 in the first shell and 4 in the second shell.
– Carbon has little tendency to form ionic bonds by loosing or gaining 4 electrons.
– Instead, carbon usually completes its valence shell by sharing electrons with other atoms in four covalent bonds.
– This tetravalence by carbon makes large, complex molecules possible.

• When carbon forms covalent bonds with four other atoms, they are stably arranged at the corners of an imaginary tetrahedron structure with bond angles near 109 o .
– While drawn flat, they are actually threedimensional.
• When two carbon atoms are joined by a double bond, all bonds around the carbons are in the same plane.
– They have a flat, three-dimensional structure.

The carbon atom forms four, spatially defined hybrid sp3-orbitals instead of the more commonly found s and p orbitals.
Tetrahedral structure of methane (CH
4
)

R
R
2
1
C
Rotational freedom
R
1
C
R
3
Covalent bonds
(fixed angles)
R
2
R
3
Angle = 109.5
o

The carbon-carbon double bond
Ethylene
Double bond
 rigid planarity
 no free rotation possible
Chemistry based on carbon allows:
1. the creation of long carbon chains serving as the backbones of multiple organic molecules.
2. the storage of high amounts of energy in the repetitive carbon-carbon bonds.
- for example, the C-C covalent bond contains 83.1 kcal (kilocalories) per mole, while a C=C double covalent bond stores about 147 kcal/mole

Different carbon skeletons

• Isomers are compounds that have the same molecular formula but different structures and therefore different chemical properties.
– For example, butane and isobutane have the same molecular formula C
4
H
10
, but butane has a straight skeleton and isobutane has a branched skeleton.
• The two butanes are structural isomers , molecules with the same molecular formula but differ in the covalent arrangement of atoms.

• Enantiomers are molecules that are mirror images of each other
– Enantiomers are possible if there are four different atoms or groups of atoms bonded to a central carbon.
– If this is true, it is possible to arrange the four groups in space in two different ways that are mirror images.
– Like left-and right-handed versions.
– Usually one is biologically active, the other inactive.

Enantiomers

Only the L-Dopa enantiomer is effective to reduce the symptoms in patients suffering from Parkinson Disease (PD), while the D-Dopa isomer is biologically inactive.

The 2 stereoisomers of the amino acid alanine
Asymmetric C-atom or
α C-atom
Only this stereoisomer of alanine is found in biological organisms

Carbon &
Functional Groups

• Cells join smaller organic molecules together to form larger molecules.
• These larger molecules, macromolecules , may be composed of thousands of atoms and weigh over 100,000 daltons.
• The four major classes of macromolecules are: carbohydrates, lipids, proteins, and nucleic acids.

• Three of the four classes of macromolecules form chainlike molecules called polymers .
– Polymers consist of many similar or identical building blocks linked by covalent bonds.
• The repeated units are small molecules called monomers .
– Some monomers have other functions of their own.

• The chemical mechanisms that cells use to make and break polymers are similar for all classes of macromolecules.
• Monomers are connected by covalent bonds via a condensation reaction or dehydration reaction .
– One monomer provides a hydroxyl group and the other provides a hydrogen and together these form water.
– Requires energy and is aided by enzymes.

• The covalent bonds connecting monomers in a polymer are disassembled by hydrolysis .
– In hydrolysis as the covalent bond is broken a hydrogen atom and hydroxyl group from a split water molecule attaches where the covalent bond used to be.
– Hydrolysis reactions dominate the digestive process, guided by specific enzymes.

• Carbohydrates include both sugars and polymers.
• The simplest carbohydrates are monosaccharides or simple sugars.
• Monosaccharides generally have molecular formulas that are some multiple of CH
2
O.
– For example, glucose has the formula C
6
H
12
O
6
.
• Disaccharides, double sugars, consist of two monosaccharides joined by a condensation reaction.
• Polysaccharides are polymers of monosaccharides.

• Monosaccharides, particularly glucose, are a major fuel for cellular work.
• They also function as the raw material for the synthesis of other monomers, including those of amino acids and fatty acids.

1. Carbohydrates
The general sum formula for the simplest carbohydrates, or also referred to as monosaccharides, is:
(CH
2
O) x n n = 3,4,5,6 or 7
Hemiacetal-
Formation
(in H
2
O)
Hexose
Haworth projections
Hexose

Anomeric forms of glucose are annotated as alpha (α) and beta (β) forms
HO CH
2
O
OH
HO
OH
α-D-Glucose
1
OH
HO CH
2
O
OH
OH 1
HO
OH
β-D-Glucose
When alpha and beta anomers of glucose become involved in polymerization reactions stereochemically different polymers, e.g. starch and cellulose, result with very different biological functions

Chemical structures of different biologically relevant hexoses
HO CH
2
O
OH
OH
HO
OH
( β-D-Glucose)
HO CH
2
O
OH
OH
OH
HO
( β-D-Mannose)
HO CH
2 O
OH
HO
CH
2
– OH
OH
( β-D-Fructose)
HO CH
2
O
OH
OH
HO
NH
2
( β-D-Glucosamine)
HO
HO
CH
2
OH
O
OH
OH
( β-D-Galactose)
HO
O
CH
3 OH
OH
OH
( β-L-Fucose)
= 6-Deoxy-
β-L-galactose

Chemical structures of different biologically relevant mono-saccharides
Triose
Pentoses
Xylose
Arabinose

Disaccharides

Disaccharides and polysaccharides are formed by dehydration synthesis involving two critical hydroxyl groups of mono sugars under release of water
 The covalent bond formed between two adjacent sugar molecules in di- and polysaccharides is also referred to as glycosidic linkage or glycosidic bond.
αlpha
α

Chemical structure of the disaccharides lactose and sucrose
Lactose
β(1  4)
β
α
α(1  2)
Sucrose

Polysaccharides & Biomass
 Polysaccharides are complex sugars made up from hundreds to millions of mono-sugars linked together via multiple glycosidic bonds
 The polysaccharides cellulose, hemicellulose and starch are produced in huge amounts by all green plants and algae during photosynthesis to form biomass in a renewable fashion
“Globally green plants convert about 190 Giga tons (190 x 10 9 tons) of carbon dioxide (CO
2
) into biomass annually.”

• Polysaccharides are polymers of hundreds to thousands of monosaccharides joined by glycosidic linkages.
• One function of polysaccharides is as an energy storage macromolecule that is hydrolyzed as needed.
• Other polysaccharides serve as building materials for the cell or whole organism.
• Important polysaccharides are: starch
(plants), cellulose (plants), and glycogen
(animals).

Cellulose

Cellulose is an unbranched polysaccharide build from glucose units
 8,000 – 12,000 glucose molecules are linked via β (1  4)-glycosidic bonds
“Cellulose can be broken down into smaller fragments, cellobiose and glucose with the help of a class of enzymes called cellulases.”

Starch
 Starch is a polysaccharide composed of glucose monomers
 It consists to 20- 30% of unbranched amylose and the rest is comprised of the branched amylopectin component
 The glucose monomers are linked via repeated 1  4-
α-glycosidic linkages
“Starch can be easily broken down into smaller amylose fragments, maltose and glucose with the help of a class of enzymes called amylases and glucoamylases.”

Starch & Human Food
 Starch is an important, high caloric component of many human staple foods, such as French fries, tortillas, noodles and rice
 Important agricultural plants store huge amounts of starch in different plant parts
Agricultural plant
1. sugar cane
2. sugar beet
3. corn
4. rice
5. Wheat
6. barley
7. potato
8. jam
Plant part of starch storage stems tuber endosperm of kernel endosperm of kernel endosperm endosperm tuber tuber

Hemicellulose
 Hemicellulose is a complex polymer comprised of the mono-sugars xylose, arabinose, galactose und fucose which is found in plant cell walls
 Hemicellulose polysaccharides, are often referred to as cross-linking glycans, since they are hydrogen bonded to the surface of the cellulose microfibrils

It is hypothesized that hemicellulose polymers tether the cellulose microfibrils

Fats & Oils
 A fat is a polymer consisting of one glycerol backbone and three covalently attached fatty acids; chemically fats are triacylglycerides (TAGs)
 They are high energy-containing molecules which serve as energy reserve and play a role in thermo-insulation

Depending on the fatty acid composition, TAGs appear as more solid fats or more viscous oils
Two saturated fatty acids
A triacylglyceride (TAG) molecule
Fatty acid Glycerol

Triacylglycerides & Biological functions
1. Protection from the metabolism lowering, negative effects of low temperatures
2. Avoidance of hypothermia in infants, hibernating mammals and whales.
3. High energy-donating reserve molecule, especially during periods of food scarcity, mal-nutrition or during stress.
4. Storage and deposit layer for certain lipophilic (= fat-loving) molecules, i.e. metabolic wastes, drugs, poisons, and pesticides

A typical phospholipid molecule
Phosphate group
Glycerol
2x Fatty acid
Space fill structure
Chemical structure
 Phospholipids consist of two fatty acids, which are covalently linked to a glycerol backbone (see pink-colored part).

The third molecular component which is covalently linked with the third hydroxyl group of the glycerol backbone can be a(n):
1. Phosphate group
2. Phosphate derivative
3. Choline
4. Ethanolamine
5. Sugar (e.g. inositol)

Polar and unpolar regions of a typical phospholipid molecule
Head
Tail

Arrangement of phospholipids in a biological (= cell) membrane
(

Lipid bilayer diagram)

Schematic picture of a segment of a biological cell membrane

Steroids

Steroids are 4-ringed, lipid-like molecules which are the starting material for the synthesis of many important biological molecules.
 Most of the steroids, for example cholesterol, are very lipophilic molecules.

Chemical structures of different steroids
H
3
C
O
1
(Testosterone)
H
3
C
OH
O
O
H
3
C
O
H
3
C
CH
2
OH
C
OH
2
(Cortisone)
H
3
H
3
C
C
CH
3
CH
3
H
3
C
HO
3
(Cholesterol)
Mammals & Humans
H
H
3
3
C
C
H
3
C
HO
4
(Ergosterol)

Yeast steroid
CH
3
CH
3
CH
3
HO
O
Glucose
Glucose
Galactose
Galactose
Xylose
H
3
C
H
3
C
H
3
C
O
O
OH
H
5
(Digitonin)

Plant glycoside
 saponine
HO
HO
CH
3 H
H
3
3
C
C
HO
OH
CH
3
CH
OH
3
H
3
C
OH
H
O 6
(Ecdysteron)

Insect steroid

“molting hormone”

Alcohols
 Alcohols are a class of compounds which contain the hydroxyl (-OH) functional group and have the general formula ROH.

An alcohol containing a
–CH
2
OH group is known as a primary alcohol.
An alcohol which contains a =CHOH group is referred to as a secondary alcohol.
An alcohol containing a ≡COH group is a tertiary alcohol.

Common alcohols are methanol, ethanol, propanol and butanol, which are alcohols containing 1,2,3, and 4 carbon atoms.
 Alcohols containing two or more hydroxyl groups are called diols, triols and so on.
Alcohol
Properties of Some Alcohols
Name Boiling Point
( o C)
CH
3
OH
CH
3
CH
2
OH
CH
3
CH
2
CH
2
OH
CH
3
CH
2
CH
2
CH
2
OH
CH
3
CH
2
CH
2
CH
2
CH
2
OH
CH
3
CH
2
CH
2
H
CH
2
CH
2
CH
2
O
Methanol
Ethanol
1-Propanol
1-Butanol
1-Pentanol
1-Hexanol
65
78
97
117
138
158
Water Solubility
(g/100ml H
2
25 o C
O); miscible miscible miscible
9.0
2.7
0.6

Amino acids & Proteins
Red
Blue
Serine Cysteine
= conserved amino and carboxy group involved in peptide bond formation
= unique part or “R- group” of the amino acid
20 amino acids have been identified in all forms of life on planet Earth, which – according to their different chemical structures - have been organized in following groups:
 basic amino acids
 acidic amino acids
=
= arginine, histidine, lysiine glutamic acid, aspartic acid, asparagine, glutamine glycine, alanine, leucin, isoleucine, valine  aliphatic amino acids
 sulfur-containing
 aromatic amino acids
 non-aromatic a. acids
=
=
=
= cysteine and methionine tyrosine, phenylalanine, tryptophan serine, threonine

Examples of hydrophobic amino acids

Amino acids & Peptide bond formation
 Amino acids can be chemically linked together by dehydration synthesis which results in the formation of a peptide bond.
 In living cells, this chemical reaction which leads to the formation of polypeptides is catalyzed by a large protein/RNA complex called a ribosome.

Hierarchical organization of proteins

The linear arrangement of amino acids in a polypeptide chain, or amino acid sequence, is also called the primary structure of a protein.
Peptide bond
 In order for a polypeptide chain to become biologically functional it has to be folded and coiled into a final, uniquely shaped 3-dimensional form, called a protein .

Hierarchical organization of proteins
 Parts of the polypeptide chain of a protein are coiled or folded into two characteristic micro-structures, referred to as secondary structures .

Important secondary structures are:
1.
Alpha-helix (plural alpha-helices)
2.
Beta-sheet (or often called pleated sheets)
 Both secondary structures of are maintained/stabilized by regular spaced hydrogen bonds between the - N – H groups and the – C = O groups at the alpha C-atom.

α
-Helix

Hydrogen bond formation between residues of the peptide bonds of amino acids forms a rigid, rod-like molecular cylinder.
R-Groups
Hydrogen
Bonds

β-Sheet (or pleated sheet)

Hydrogen bonding between backbone atoms of amino acids of adjacent

-sheets form a rigid, planar, sheet-like structure in proteins.
R-Groups
Hydrogen
Bonds
Polypeptide 1
Polypeptide 2
Pleated or beta sheets in a protein

Hierarchical organization of proteins

The 3-dimensional structure of a protein is referred to as the tertiary structure .
 The final 3-dimensional structure of a protein is strongly dependent on:
1. The linear sequence of its amino acids and
2. The chemical properties of the side groups (R) of its amino acids
“The 3-dimensional protein structure determines the protein’s unique biological function…”
α-
Helix
β-Sheet
Loops/Turns
Computer-assisted ribbon model of the mitochondrial IDH protein depicting the “run” of the polypeptide chain

Hierarchical organization of proteins

When multiple polypeptide chains or protein sub-units interact to form to form the final functional protein complex, we speak of a quaternary structure .
 Examples are: Hemoglobin, Growth factor receptors and Immunoglobulins.

Nucleotides & Nucleic acids
 Nucleic acids are made up from nitrogen-containing chemical monomers, called nucleotides .

The sequence of nucleotides in nucleic acids codes for the genetic information of proteins.
 The nucleic acid DNA is the blueprint molecule of all forms of life on planet Earth.

2 types of nucleic acids are known:
1. Dexoyribonucleic acid (DNA
the hereditary molecule coding for the “molecular blueprint” of life
2. Ribonucleic acid (RNA)
- different types are known, e.g. rRNA, tRNA, mRNA and microRNA, each with different biological functions
The nucleotide Cytosine

The nucleic acid DNA
HO
Deoxyribose
“Purines”
“Pyrimidines”

Four nucleotides

A, T, C and G make up DNA

Sugar
Nucleotides
Comparison of the RNA and DNA molecules
Ribose Deoxyribose
(A, U, G, C) (A, T, G, C)

Biomass
 Biomass is a direct product of a biological process called photosynthesis.
 During photosynthesis, sunlight is captured by plants and algae with the help of chlorophyll molecules and used as energy source for fixation of CO
2 in the chemical bonds of the many carbon compounds.
“Biomass is defined as all non-fossil-based living or dead organisms and organic materials that regrow and have an intrinsic chemical energy content.
Examples of biomass are dead or live leaves, stems, branches or trunks of trees, shrubs, grasses, animal fat and protein and algae.”